Impossible to install

[assignUser]

It is currently impossible to conda install adel because the binaries/dependencies (like plantgl) don't exists (windows) or were build against an 8 year old glibc version (linux) which makes them impossible to run on any updated system.

I am currently building all dependencies manually and editing the meta.yaml in hope of getting this to work.
Should I have missed an easy solution for this issue I will happily close it.

Edit: this might be more of an issue with plantgl...

[assignUser]

I just saw that you have a channel with all the dependencies up to date.

[HowcanoeWang]

I just saw that you have a channel with all the dependencies up to date.

Could give more detail about that "channel"? (any links or url?) I met the same problem...

[assignUser]

@HowcanoeWang Hey, I found it here: #23
But I did not manage to install it anyway... :(

[HowcanoeWang]

@assignUser Many thanks! I fought with it the whole night, and decided not use it either :(

[pradal]

At the end, do you succeed to install Adel?
@mlabadie @christian34 : any insights?

[HowcanoeWang]

At the end, do you succeed to install Adel? @mlabadie @christian34 : any insights?

It seems there are very complex dependency version conflicts that exist via conda, and I also tried python package/setup.py install from source code, neither succeed yet.

Please check this issue: #28

[assignUser]

@pradal No i tried several different times over several days including manually compiling missing/old dependecies and editing meta.yamls but gave up as there were new conflicts/issues after every fixed problem...

[pradal]

Thks for your patience. @mlabadie is currently documenting a way to install Adel.
Stay tuned!

[mlabadie]

@assignUser, @HowcanoeWang Sorry for the delay. I update the documentation on branch Port_python_3

To install adel you can follows this ways:

• conda installation

conda create -n adel -c conda-forge python=3.8 ipython numpy=1.20 pandas rpy2 scipy setuptools=49.6 path -y

• activate adel environment:
  conda activate adel

• conda installation of packages
  conda install -c fredboudon -c conda-forge openalea.plantgl openalea.mtg -y

• install others package from git

  • openalea.deploy package:

  git clone https://github.com/openalea/deploy.git;
  cd deploy;
  python setup.py install
  cd..
  

  • adel package

  git clone -b Port_python_3 https://github.com/openalea-incubator/adel.git
  cd adel
  python setup.py develop
  

[assignUser]

@mlabadie Thank you, I could install it now without issue. But I can not run any of the examples, after fixing a few encoding issues I got this error KeyError: "'setAdelArv' not found" Which could be "fixed" by commenting out the line trying to set that envvar in AdelR.py which led to:

Traceback (most recent call last):
  File "test_AdelWheat.py", line 2, in <module>
    from alinea.astk.Weather import sample_weather

[HowcanoeWang]

@mlabadie Thanks for your feedback, now it has been successfully installed on my Mac.

@assignUser I met the same encoding problem for Adel.R problem when I run the from alinea.adel.astk_interface import AdelWheat, you could fix it by editing the AdelR.py line 47 to with open(os.path.join(dir,file_name), 'r', encoding="latin-1") as content_file: without commenting out anything.

But still get import error:

Traceback (most recent call last):
  File "test_wheat.py", line 2, in <module>
    from alinea.astk.Weather import sample_weather
ModuleNotFoundError: No module named 'alinea.astk'

[assignUser]

@HowcanoeWang I used iconv to change the encoding of the file to utf-8.

[NieJL1CN]

@assignUser @HowcanoeWang Have you solved these problems yet? I changed the encoding of the file and installed alinea.atsk via conda then the test_Adelwheat.py is somehow running with the error R[write to console]: collapsing to unique 'x' values, so I still can't get the simulation. When I run the other examples, they all have errors too. Referring to other openalea project manuals like Lgrass, I thought I should get a visual wheat virtual model that I could view via openalea.lpy, but in fact that didn't work either.

[pradal]

We are currently releasing all the stack on a new channel openalea3.
We will test the full suite in the nextdays/week.

@mlabadie @christian34

[assignUser]

@NieJL1CN I haven't made any other attempts :( But it sounds like there will be a solution soon!

[pradal]

Hi @assignUser @NieJL1CN @HowcanoeWang

I just release a new version on openalea3 channel in anaconda.org.
You can test the installation with

conda create -n adel alinea.adel -c openalea3 -c conda-forge

[HowcanoeWang]

Hi @assignUser @NieJL1CN @HowcanoeWang

I just release a new version on openalea3 channel in anaconda.org. You can test the installation with

conda create -n adel alinea.adel -c openalea3 -c conda-forge

Yes, it seems no problem to install in my WSL2 ubuntu environment

PS: but I got an error when try the following example code:

>>> from alinea.adel.astk_interface import AdelWheat
>>> from alinea.astk.Weather import sample_weather

>>> adel = AdelWheat(nsect=2)
>>> g = adel.setup_canopy(100)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/hwang/miniconda3/envs/adel/lib/python3.9/site-packages/alinea.adel-1.9.0-py3.9.egg/alinea/adel/astk_interface.py", line 154, in setup_canopy
    g = self.build_mtg(canopy, stand,
  File "/home/hwang/miniconda3/envs/adel/lib/python3.9/site-packages/alinea.adel-1.9.0-py3.9.egg/alinea/adel/adel.py", line 226, in build_mtg
    g = mtg_factory(parameters, stand=stand, leaf_sectors=self.nsect,
  File "/home/hwang/miniconda3/envs/adel/lib/python3.9/site-packages/alinea.adel-1.9.0-py3.9.egg/alinea/adel/newmtg.py", line 532, in mtg_factory
    if args.get('HS_final') < args.get('nff'):
TypeError: '>' not supported between instances of 'numpy.ndarray' and 'numpy.str_'

[pradal]

Thanks.
I will close this issue and open a new one.
This problem is the same that #29